Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: R9478

Calculation Name: 3NCY-W-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NCY

Chain ID: W

ChEMBL ID:

UniProt ID: P60066

Base Structure: X-ray

Registration Date: 2023-06-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2121948.829832
FMO2-HF: Nuclear repulsion 2039025.421728
FMO2-HF: Total energy -82923.408104
FMO2-MP2: Total energy -83160.673631


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(W:1:GLU)


Summations of interaction energy for fragment #1(W:1:GLU)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-36.522-33.2030.944-1.702-2.560.006
Interaction energy analysis for fragmet #1(W:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.938 / q_NPA : -0.979
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3W3VAL00.019-0.0123.805-3.671-1.968-0.023-0.719-0.9610.004
4W4MET00.0320.0235.848-2.673-2.6730.0000.0000.0000.000
5W5THR0-0.017-0.0139.171-1.815-1.8150.0000.0000.0000.000
6W6GLN00.0570.04711.495-0.031-0.0310.0000.0000.0000.000
7W7SER0-0.0430.00414.723-0.212-0.2120.0000.0000.0000.000
8W8PRO00.0560.01218.209-0.137-0.1370.0000.0000.0000.000
9W9ALA00.0540.01918.8790.2090.2090.0000.0000.0000.000
10W10ILE0-0.003-0.00819.836-0.027-0.0270.0000.0000.0000.000
11W11MET0-0.0280.00123.340-0.002-0.0020.0000.0000.0000.000
12W12SER00.004-0.00726.148-0.158-0.1580.0000.0000.0000.000
13W13ALA00.0030.01829.628-0.020-0.0200.0000.0000.0000.000
14W14SER0-0.013-0.00832.044-0.106-0.1060.0000.0000.0000.000
15W15PRO00.019-0.00635.0700.1180.1180.0000.0000.0000.000
16W16GLY00.0170.01835.905-0.203-0.2030.0000.0000.0000.000
17W17GLU-1-0.924-0.95432.5868.9308.9300.0000.0000.0000.000
18W18LYS10.9860.99830.469-9.040-9.0400.0000.0000.0000.000
19W19VAL00.0100.00926.0870.1440.1440.0000.0000.0000.000
20W20THR0-0.061-0.05324.205-0.026-0.0260.0000.0000.0000.000
21W21MET0-0.0100.02620.4620.1780.1780.0000.0000.0000.000
22W22THR0-0.020-0.02118.6240.2120.2120.0000.0000.0000.000
23W23CYS0-0.084-0.03613.2440.5490.5490.0000.0000.0000.000
24W24SER0-0.0130.02713.327-0.083-0.0830.0000.0000.0000.000
25W25ALA00.0720.01410.0860.6130.6130.0000.0000.0000.000
26W26SER0-0.084-0.0265.442-1.321-1.3210.0000.0000.0000.000
27W27SER00.0410.0137.314-0.824-0.8240.0000.0000.0000.000
28W28SER0-0.008-0.0159.847-0.498-0.4980.0000.0000.0000.000
29W29VAL0-0.0180.0009.3581.1261.1260.0000.0000.0000.000
30W30ASN00.000-0.00411.890-0.985-0.9850.0000.0000.0000.000
31W36TYR0-0.048-0.00814.418-0.165-0.1650.0000.0000.0000.000
32W37MET00.0010.01211.5651.4071.4070.0000.0000.0000.000
33W38HIS0-0.014-0.00513.981-1.742-1.7420.0000.0000.0000.000
34W39TRP00.0610.01415.8040.8120.8120.0000.0000.0000.000
35W40TYR0-0.031-0.01515.140-1.149-1.1490.0000.0000.0000.000
36W41GLN0-0.0020.00319.6720.1520.1520.0000.0000.0000.000
37W42GLN0-0.047-0.02919.5980.0860.0860.0000.0000.0000.000
38W43LYS10.9330.97022.426-9.811-9.8110.0000.0000.0000.000
39W44SER00.0710.03425.705-0.172-0.1720.0000.0000.0000.000
40W45GLY00.0110.01622.809-0.229-0.2290.0000.0000.0000.000
41W46THR0-0.062-0.03323.1880.3440.3440.0000.0000.0000.000
42W47SER00.0260.00822.4470.4030.4030.0000.0000.0000.000
43W48PRO00.0220.00418.534-0.436-0.4360.0000.0000.0000.000
44W49LYS10.9680.99921.391-10.846-10.8460.0000.0000.0000.000
45W50ARG10.9450.97121.354-10.560-10.5600.0000.0000.0000.000
46W51TRP0-0.035-0.03421.625-0.561-0.5610.0000.0000.0000.000
47W52ILE00.0000.00320.508-0.414-0.4140.0000.0000.0000.000
48W53TYR00.0180.02519.2600.7040.7040.0000.0000.0000.000
49W54ASP-1-0.815-0.94818.66512.89912.8990.0000.0000.0000.000
50W55THR0-0.0260.00618.332-0.245-0.2450.0000.0000.0000.000
51W56SER0-0.058-0.04619.815-0.288-0.2880.0000.0000.0000.000
52W57LYS10.8940.97222.992-12.008-12.0080.0000.0000.0000.000
53W58LEU00.0410.02424.1160.3950.3950.0000.0000.0000.000
54W59ALA0-0.035-0.01725.000-0.090-0.0900.0000.0000.0000.000
55W60SER0-0.004-0.01226.710-0.106-0.1060.0000.0000.0000.000
56W61GLY0-0.009-0.00429.969-0.216-0.2160.0000.0000.0000.000
57W62VAL0-0.051-0.00226.322-0.149-0.1490.0000.0000.0000.000
58W63PRO00.0360.03329.724-0.158-0.1580.0000.0000.0000.000
59W64ALA00.041-0.00731.0120.2270.2270.0000.0000.0000.000
60W65ARG10.8180.90131.611-8.804-8.8040.0000.0000.0000.000
61W66PHE00.0460.01825.8140.1460.1460.0000.0000.0000.000
62W67SER0-0.0010.00026.694-0.161-0.1610.0000.0000.0000.000
63W68GLY00.0130.01622.8590.2650.2650.0000.0000.0000.000
64W69SER0-0.034-0.01922.020-0.384-0.3840.0000.0000.0000.000
65W70GLY00.0600.02019.8550.5040.5040.0000.0000.0000.000
66W71SER0-0.036-0.03218.031-0.339-0.3390.0000.0000.0000.000
67W72GLY00.0580.03915.401-0.006-0.0060.0000.0000.0000.000
68W73THR00.0130.00412.4890.6720.6720.0000.0000.0000.000
69W74SER0-0.0250.00514.3980.3950.3950.0000.0000.0000.000
70W75TYR00.001-0.00714.508-1.123-1.1230.0000.0000.0000.000
71W76SER0-0.025-0.03018.0030.0420.0420.0000.0000.0000.000
72W77LEU0-0.0300.01420.345-0.311-0.3110.0000.0000.0000.000
73W78THR0-0.036-0.02622.327-0.177-0.1770.0000.0000.0000.000
74W79ILE00.0340.00125.989-0.017-0.0170.0000.0000.0000.000
75W80SER0-0.066-0.02629.268-0.059-0.0590.0000.0000.0000.000
76W81SER00.0150.01432.773-0.075-0.0750.0000.0000.0000.000
77W82MET0-0.039-0.00230.7230.2030.2030.0000.0000.0000.000
78W83GLU-1-0.874-0.95332.3607.8497.8490.0000.0000.0000.000
79W84ALA00.0240.00832.5650.2520.2520.0000.0000.0000.000
80W85GLU-1-0.934-0.98332.3938.7038.7030.0000.0000.0000.000
81W86ASP-1-0.782-0.87328.8759.7799.7790.0000.0000.0000.000
82W87ALA00.0110.02627.5080.4730.4730.0000.0000.0000.000
83W88ALA0-0.024-0.02824.976-0.036-0.0360.0000.0000.0000.000
84W89THR0-0.0120.01419.0750.1240.1240.0000.0000.0000.000
85W90TYR0-0.043-0.02920.0040.0320.0320.0000.0000.0000.000
86W91TYR0-0.010-0.01114.3030.5080.5080.0000.0000.0000.000
87W93GLN00.018-0.00611.335-0.042-0.0420.0000.0000.0000.000
88W94GLN00.0790.0235.995-1.803-1.8030.0000.0000.0000.000
89W95TRP00.004-0.0098.7521.3371.3370.0000.0000.0000.000
90W96SER0-0.026-0.0049.447-1.057-1.0570.0000.0000.0000.000
91W97TYR00.0000.0045.295-0.397-0.3970.0000.0000.0000.000
92W98ASN00.0010.0255.046-3.308-3.3080.0000.0000.0000.000
93W99PRO0-0.001-0.0212.6631.4362.8600.968-0.956-1.4360.002
94W100PRO00.0340.0364.9982.3992.448-0.001-0.002-0.0460.000
95W101THR0-0.043-0.0254.0450.2220.3650.000-0.025-0.1170.000
96W102PHE00.014-0.0177.461-2.967-2.9670.0000.0000.0000.000
97W103GLY00.0300.0028.9551.8411.8410.0000.0000.0000.000
98W104GLY0-0.051-0.02911.378-0.150-0.1500.0000.0000.0000.000
99W105GLY00.0080.00813.242-0.695-0.6950.0000.0000.0000.000
100W106THR0-0.048-0.02216.3030.0720.0720.0000.0000.0000.000
101W107LYS10.8910.93719.524-11.823-11.8230.0000.0000.0000.000
102W108LEU00.011-0.00222.541-0.194-0.1940.0000.0000.0000.000
103W109GLU-1-0.854-0.94025.68910.32210.3220.0000.0000.0000.000
104W110ILE00.0500.01729.058-0.055-0.0550.0000.0000.0000.000
105W111LYS10.9020.96132.564-8.789-8.7890.0000.0000.0000.000
106W112ARG10.8500.92834.984-7.641-7.6410.0000.0000.0000.000
107W113ALA0-0.015-0.01338.5010.0490.0490.0000.0000.0000.000
108W114ASP-1-0.860-0.93739.6337.7397.7390.0000.0000.0000.000
109W115ALA0-0.0100.00341.476-0.186-0.1860.0000.0000.0000.000
110W116ALA00.0290.00642.4320.1610.1610.0000.0000.0000.000
111W117PRO0-0.019-0.01242.443-0.033-0.0330.0000.0000.0000.000
112W118THR0-0.0160.01144.419-0.209-0.2090.0000.0000.0000.000
113W119VAL0-0.027-0.01945.3270.0380.0380.0000.0000.0000.000
114W120SER0-0.0160.00246.876-0.222-0.2220.0000.0000.0000.000
115W121ILE0-0.015-0.01347.4030.1610.1610.0000.0000.0000.000
116W122PHE0-0.014-0.01147.811-0.122-0.1220.0000.0000.0000.000
117W123PRO00.0100.00950.0040.0780.0780.0000.0000.0000.000
118W124PRO0-0.021-0.01150.4100.0750.0750.0000.0000.0000.000
119W125SER00.0410.02050.562-0.110-0.1100.0000.0000.0000.000
120W126SER00.0750.00752.6150.0000.0000.0000.0000.0000.000
121W127GLU-1-0.898-0.94151.7795.9395.9390.0000.0000.0000.000
122W128GLN0-0.0400.00047.6110.2290.2290.0000.0000.0000.000
123W129LEU00.0040.00251.565-0.006-0.0060.0000.0000.0000.000
124W130THR0-0.062-0.02654.422-0.063-0.0630.0000.0000.0000.000
125W131SER0-0.045-0.02651.0610.0050.0050.0000.0000.0000.000
126W132GLY0-0.0040.01551.4290.0720.0720.0000.0000.0000.000
127W133GLY00.0100.00949.1170.1090.1090.0000.0000.0000.000
128W134ALA0-0.016-0.01349.022-0.130-0.1300.0000.0000.0000.000
129W135SER00.0310.00745.5000.1670.1670.0000.0000.0000.000
130W136VAL0-0.026-0.00147.194-0.083-0.0830.0000.0000.0000.000
131W137VAL00.0440.03143.8940.1900.1900.0000.0000.0000.000
132W138CYS0-0.112-0.05544.124-0.108-0.1080.0000.0000.0000.000
133W139PHE0-0.033-0.01642.0850.1930.1930.0000.0000.0000.000
134W140LEU00.0130.00841.073-0.154-0.1540.0000.0000.0000.000
135W141ASN00.0520.00840.9010.2940.2940.0000.0000.0000.000
136W142ASN00.0100.00040.728-0.196-0.1960.0000.0000.0000.000
137W143PHE0-0.0350.00636.776-0.147-0.1470.0000.0000.0000.000
138W144TYR00.0120.01833.4630.2490.2490.0000.0000.0000.000
139W145PRO00.029-0.00334.763-0.174-0.1740.0000.0000.0000.000
140W146LYS10.9080.94928.099-10.553-10.5530.0000.0000.0000.000
141W147ASP-1-0.914-0.95533.0249.2779.2770.0000.0000.0000.000
142W148ILE00.0000.00234.984-0.301-0.3010.0000.0000.0000.000
143W149ASN00.0210.01336.9850.1930.1930.0000.0000.0000.000
144W150VAL00.0100.02639.278-0.185-0.1850.0000.0000.0000.000
145W151LYS10.8970.94141.340-7.600-7.6000.0000.0000.0000.000
146W152TRP00.0560.00938.161-0.007-0.0070.0000.0000.0000.000
147W153LYS10.8420.94644.052-7.094-7.0940.0000.0000.0000.000
148W154LYS10.9880.96446.735-6.283-6.2830.0000.0000.0000.000
149W155ILE0-0.032-0.00250.238-0.045-0.0450.0000.0000.0000.000
150W156ASP-1-0.710-0.89152.8145.5895.5890.0000.0000.0000.000
151W157GLY0-0.051-0.01554.626-0.063-0.0630.0000.0000.0000.000
152W158SER00.003-0.00452.1060.0870.0870.0000.0000.0000.000
153W159GLU-1-0.940-0.96347.1336.7526.7520.0000.0000.0000.000
154W160ARG10.9171.00444.690-6.898-6.8980.0000.0000.0000.000
155W161GLN00.0430.00939.994-0.069-0.0690.0000.0000.0000.000
156W162ASN0-0.012-0.03240.1670.2190.2190.0000.0000.0000.000
157W163GLY00.0630.02640.446-0.192-0.1920.0000.0000.0000.000
158W164VAL0-0.054-0.02139.496-0.096-0.0960.0000.0000.0000.000
159W165LEU0-0.0060.00437.0130.2660.2660.0000.0000.0000.000
160W166ASN00.0320.00835.434-0.324-0.3240.0000.0000.0000.000
161W167SER0-0.026-0.00433.3990.2770.2770.0000.0000.0000.000
162W168TRP0-0.014-0.02031.714-0.272-0.2720.0000.0000.0000.000
163W169THR00.0010.00432.2110.1980.1980.0000.0000.0000.000
164W170ASP-1-0.999-0.98628.36910.51310.5130.0000.0000.0000.000
165W171GLN00.010-0.03431.0520.1840.1840.0000.0000.0000.000
166W172ASP-1-0.858-0.90633.2317.9037.9030.0000.0000.0000.000
167W173SER0-0.020-0.02434.469-0.029-0.0290.0000.0000.0000.000
168W174LYS10.9040.94335.889-7.260-7.2600.0000.0000.0000.000
169W175ASP-1-0.806-0.88338.8727.4317.4310.0000.0000.0000.000
170W176SER0-0.021-0.00135.7440.0340.0340.0000.0000.0000.000
171W177THR0-0.117-0.05836.3300.0880.0880.0000.0000.0000.000
172W178TYR00.0460.00931.1650.2600.2600.0000.0000.0000.000
173W179SER00.0370.00736.192-0.334-0.3340.0000.0000.0000.000
174W180MET0-0.043-0.01336.2570.2120.2120.0000.0000.0000.000
175W181SER00.0080.01537.497-0.317-0.3170.0000.0000.0000.000
176W182SER00.0130.00638.4480.1170.1170.0000.0000.0000.000
177W183THR0-0.011-0.01640.102-0.305-0.3050.0000.0000.0000.000
178W184LEU0-0.033-0.02841.9430.1330.1330.0000.0000.0000.000
179W185THR00.0090.00243.331-0.105-0.1050.0000.0000.0000.000
180W186LEU0-0.045-0.02645.1580.0740.0740.0000.0000.0000.000
181W187THR00.0530.03147.5740.0650.0650.0000.0000.0000.000
182W188LYS10.8990.95750.368-5.650-5.6500.0000.0000.0000.000
183W189ASP-1-0.891-0.94853.5835.7605.7600.0000.0000.0000.000
184W190GLU-1-0.865-0.96150.5326.0906.0900.0000.0000.0000.000
185W191TYR0-0.024-0.02652.626-0.029-0.0290.0000.0000.0000.000
186W192GLU-1-0.961-1.00054.2855.3605.3600.0000.0000.0000.000
187W193ARG10.8860.96956.220-5.599-5.5990.0000.0000.0000.000
188W194HIS0-0.059-0.02555.028-0.027-0.0270.0000.0000.0000.000
189W195ASN0-0.072-0.05157.5650.0360.0360.0000.0000.0000.000
190W196SER00.0120.04156.827-0.001-0.0010.0000.0000.0000.000
191W197TYR00.0400.04951.0020.1750.1750.0000.0000.0000.000
192W198THR00.007-0.00151.336-0.061-0.0610.0000.0000.0000.000
193W200GLU-1-0.864-0.94847.1026.3016.3010.0000.0000.0000.000
194W201ALA00.0710.02243.8170.1610.1610.0000.0000.0000.000
195W202THR0-0.057-0.02742.848-0.074-0.0740.0000.0000.0000.000
196W203HIS00.0480.03638.698-0.003-0.0030.0000.0000.0000.000
197W204LYS10.9910.99838.063-8.047-8.0470.0000.0000.0000.000
198W205THR0-0.045-0.03542.194-0.080-0.0800.0000.0000.0000.000
199W206SER0-0.027-0.02144.354-0.180-0.1800.0000.0000.0000.000
200W207THR0-0.015-0.00346.1690.0870.0870.0000.0000.0000.000
201W208SER0-0.032-0.00847.712-0.028-0.0280.0000.0000.0000.000
202W209PRO00.009-0.00647.4830.0310.0310.0000.0000.0000.000
203W210ILE00.0000.02147.573-0.162-0.1620.0000.0000.0000.000
204W211VAL0-0.0060.00048.3760.1250.1250.0000.0000.0000.000
205W212LYS10.9090.95650.132-6.143-6.1430.0000.0000.0000.000
206W213SER0-0.019-0.04151.5050.0560.0560.0000.0000.0000.000
207W214PHE0-0.049-0.02152.641-0.045-0.0450.0000.0000.0000.000
208W215ASN00.0570.03156.0790.1170.1170.0000.0000.0000.000
209W216ARG10.9260.98557.079-5.531-5.5310.0000.0000.0000.000